


Things we've never seen before

by liionne



Category: Star Trek: Alternate Original Series (Movies)
Genre: M/M, Missing Scene, hopefully not a lot, some canon divergence
Language: English
Status: In-Progress
Published: 2013-09-20
Updated: 2013-10-29
Packaged: 2017-12-27 04:09:47
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 4
Words: 3,734
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/974157
Author URL: https://archiveofourown.org/users/liionne/pseuds/liionne
Summary: <blockquote class="userstuff">
              <p>A collection of missing scenes from Star Trek Into Darkness.</p>
            </blockquote>





	1. I. Nibiru

**Author's Note:**

> May be some canon divergence in here, but I've tried to stick to the actual film as best I could.

"Captain, we cannot go down there. If they see us, we will corrupt their delevopment-"

"They're not going to see us, Spock."

"Well will be violating the Prime Directive-"

" _Spock!_  They're not going to see us! We're under the god damn ocean! Unless they enjoy suba diving, I think we'll be fine."

Spock gave that usual pursed-lip look he did when Jim was doing something he didn't like, and Bones sort of understood. For someone who liked the rules so much, potentially breaking Starfleet's golden rule was pretty hard.

"We'll be saving lives, Spock." Jim said, folding his arms across his chest.

Spock's stared at Jim, and Bones felt a weird sort of tension in his stomach that he really didn't like.

"The needs of the many outweigh the needs of the few."

The words were strange coming from Bones' mouth, but they had the desired effect. Spock's head turned a quarter circle like lightning, before giving McCoy an unnervingly level look.

Spock's shoulders gave just a little, losing some of their stiffness. It wasn't something you'd notice unless you were looking for it. It was one of his little human mannerisms that gave his thoughts away.

"Are you with me, Spock?" Jim asked.

Bones thought he would've sighed if it wasn't such a human gesture. "Yes, Captain." He answered, hands still clasped tightly behind his back.

"Awesome." Jim grinned. "You go up to the shuttle bay with Sulu and Uhura; we'll send you down into the volcano to neutralise it. Bones-" Jim looked over at him, and his eyes gave a twinkle that Bones knew all too well. They were about to get in trouble. "Suit up."

He clapped his hand on his shoulder as he walked past, but didn't neglect to smack his ass when Spock began to walk away.

~*~

The wetsuit was tight fighting in all the wrong - or from Jim's perspective, right, no doubt - places. He felt itchy, like he wanted to peel away the tight silver material, but it was this or getting wet for real.

And anyway, with the way Jim was looking at his ass he figured if he took the wet suit off, he might jump him then and there.

"Take a god damn picture, it'll last longer." He muttered, as he pulled pair of trousers and then the loose fitting, floaty robe over his head.

"Would if I could Bones," Jim muttered, his eyes lingering on his ass right up until it went out of sight. "Would if I could."

"Captain?"

Scotty's voice crackled over the comm, and Bones wondered if he'd been listening to them.

"Captain? The shuttle's ready, just waiting on you and Dr. McCoy."

Jim gave an almost rueful smile, and pressed the red button on the comm. "On our way." he replied.

He did take a spare moment to square up to Bones, to align them at the shoulders and the waist and the knees. He got so close to Bones that it took all of his will-power not to push him over and kiss him right there, and it didn't get any easier when Jim smirked, and took a step back.

"Best be going." He murmured. "Got a planet to save."

"Not again." Bones returned, voice barely above a whisper.

Jim chuckled lowly as he stepped away, obviously expecting Bones to follow. "Just don't take that wetsuit off until we get back to your quarters."

"Is that an order?" McCoy raised an eyebrow.

"Damn right it is." Jim smirked as he left the room.

~*~

"Alright, so this is the plan. We go in there, we move the natives away from the blast zone, and then we send Spock down with his super ice cube to freeze things over down there. And then we get back to the Enterprise, and we go home. Any questions?"

"Captain, the shuttle's not built for that kind of heat-"

"Work it out, Sulu."

Bones rolled his eyes. Apparently, Jim Kirk believed that anything was possible so long as he willed it. But then, Bones had known that for a very long time.

"Sulu, bring us round the back of the volcano; stay low, try to keep out of sight. Bones and I'll get out there."

"Aye Captain."

"Spock, Uhura- stick to the plan."

"Yes Captain."

It seemed so easy; move locals, cool volcano, go home. But of course, things never went to plan.

They were winched down for lack of better options on that horrible little shuttle, both clinging to each other in a way that looked more than friendly. Most people knew about their relationship now anyway; hell, even Spock had worked it out. Jim kept his legs wrapped around Bones' waist, and Bones kept his arms around Jim's shoulders.

When they were safely on the ground, the rope was pulled back up, and they watched as the shuttle flew away.

"Guess it's just us now." Bones muttered, staring at the sky.

"Just how we like it." Jim grinned a little, before he began to stomp through the grass and into the forest. "C'mon, Bones."

~*~

"Alright Bones, this is the plan."

Jim was full of god damn plans, Bones grumbled in his mind. Plans to get them both killed. Or worse.

What was worse than being killed?

Alright now he was off topic. He focused, shaking his head a little.

"I'm gonna go into that temple there and try to get them out. You, meanwhile, are gonna find us something we can ride so that we can get out of here before the shit starts raining down-"

"Got it." Bones nodded.

"Just come back the way you came - we'll find each other." Jim nodded.

His face was oddly serious, and so Bones ducked in to press a kiss to his lips. It was quick, and soft, and it made Jim smile. "We always do." He nodded. He looked around himself before pulling the hood over his face. "See you soon."

~*~

He'd managed to find some sort of native looking animal, and then he'd managed to climb onto it and push it forward, forcing it in the direction of the temple. He knew they were getting far too close to erruption to be happy, so her urged the beast even further forward.

And then he was thrown off and the thing fell over, groaning as it did.

Growling, Leonard pulled the hood from his robe. "Dammit, man! That was our ride. You just stunned our ride!"

Jim's nose wrinkled. "Great." he muttered. He was holding something hefty looking in his hand, and Bones wasn't sure he liked the look of it.

"Run!" Jim yelled, hearing the angry shouts from the natives behind the two of them.

Bones needed no further prompt - he ran as fast as his long legs would carry him, pushing himself throught he forest even when fatigue- because he'd been walking for ages, damn it - hit him. He could hear people ebhind them, yelling in a language he didn't understand.

"What the hell did you take!?" He yelled over at Jim, eyeing the cylinder in his hand.

"I have no idea, but they were bowing to it!" Jim returned, and Bones could have killed him.

Trust him to steal something sacred.

"Kirk to Shuttle One, the locals are out of the kill zone! You're clear, I repeat, get in there and neutralize the volcano, lets get out of here!" Jim yelled into his comm, still running just as fast as Bones was.

~*~

After a minor argument over the prime directive with Spock, they were till running, and Bones thought he might pass out. He was old, god damn it, he wasn't used to this sort of continuous exercise. He'd have to get himself to the gym sometime, if he ever found the time.

At least he could use work as an excuse not to go.

"They're trying to kill us! They're trying to kill us, Jim!" He yelled after him, as if it wasn't obvious. A spear sailed past his ear, and he muttered a few choice curse words at the back of Jim's head.

By this point, the only thing pulling him forward was how much he wanted to strangle Jim. He was pretty sure the only thing pushing Jim forward was _knowing_ how much Bones wanted to strangle him.

Sulu's voice came over the comm, and Bones just barely heard it. "Captain, I'm ditching the shuttle. You gotta make it to the Enterprise on your own."

"Wonderful." Jim heaved a heavy sigh, and they kept running forward.

Bones couldn't help but notice that it was in the wrong direction.

"Jim! Jim the beach is that way!" Bones yelled.

He had a bad feeling about this.

"We're not going to the beach!" Jim called back.

Bones felt his stomach flip.

"Oh no, no no no!" He protested, but he didn't stop running. He'd follow Jim Kirk to the edge of the Earth; following him to the edge of a cliff was nothing.

Jim hooked the scroll onto a tree branch, and Bones had to dodge it as it unravelled itself. Screeches errupted from the natives behind them, and Bones grit his teeth.

"I hate this!" He cried.

The edge of the cliff was right in sight.

Jim had time to yell before they reached the edge. "I know you do!"

And somehow, as they fell, they managed to entwine their hands together.


	2. II. Spock's Unknowing Insubordination

**Summary for the Chapter:**

> The Enterprise is taken from Jim, and Bones is there to make it better. Or rather, make Jim better.

**Notes for the Chapter:**

> In my head there was two ways this little scene could go- angry or miserable. So I kind of combined the two; I just hope it worked!

"Bones, they took her away from me."

Bones looked up at him from the couch, and his eyebrows knitted together in confusion. Jim sounded angry, unbelievably so - Bones was pretty sure he'd never seen Jim this angry before. There were tears at the corners of his eyes; it'd been a while since Jim had been more than 'quite annoyed', and Bones had almost forgotten that he cried when he was angry.

It was pretty backward really, seeing as it only made him more angry.

Jim threw himself down on the sofa next to Bones, his teeth grit together and his jaw an angry line. He flung his uniform cap across the room, and it hit the wall with a dull thud.

"We takin' it out on the apartment now?" Bones asked, raising an eyebrow.

"They took my ship, Bones." Jim muttered.

Bones leaned forward, and then he paused. He knew they'd violated the Prime Directive, of course he did - the whole damn crew knew. But they'd all assumed that there was a silent rule amongst them, saying not to mention it. Don't deny it, but don't talk about it. It was an understanding amongst the crew.

Apparently not with some.

"How?" Bones asked, his voice quietly.

"That pointy-eared bastard-" He pressed his lips into a thin line, and a tear rolled down his cheek. Bones winced as Jim growled; the angry-crying really did only make him more angry. He wanted to wipe the tear away, but drawing attention to it would only make it worse. "Spock filed a report."

Understanding hit Bones, and he sighed. "I guess he didn't spare any details?"

"Not a damn one." Jim spat, staring angrily at the wall.

Bones stared at Jim staring at the wall, and then he sighed. In one swift, and very practiced, movement, he pulled Jim over into a lying position, and rested his head in his lap. His hands found Jim's hair, long fingers lacing between the thin sandy strands. He knew the whole hair-stroking thing soothed Jim, sort of like a cat, and Bones felt a little of the tension in his shoulders dissipate at the contact.

Jim sighed, and Bones felt a small damp patch growing on his knee as Jim gave an angry sniffle. Jim curled up, assuming a foetal position on the sofa.

"I could kill him." Jim muttered, although his voice sounded more weak than angry, now.

"I know darlin'." Bones murmured, running his hand through his hair.

Jim gave another sniffle. "What I'm gonna do, Bones? The ship, the crew-" He paused, and Bones didn't even want to imagine the look on his face. "They're the only family I've got."

"You've still got me, Jim." Bones said, his voice still soft. "You've always got me."

That seemed to silence Jim, for a little while. "Hang around me like a bad smell." He said, looking up to give Bones a small, watery grin.

"Damn right." Bones murmured, grinning right back at him.

Jim sat up, and pressed the gentlest of kisses to Bones' lips. "Thank you." He whispered.

Bones wrapped his arms around him, holding Jim's body close to his own. "Everything's gonna be alright, Jim." He murmured, pressing a kiss to his temple. "Everything's gonna be fine."


	3. III. Jim is an angry drunk

**Summary for the Chapter:**

> Bones arrives home after Pike's death, and finds a bit of a mess.

Bones knew he was too late when he got there; he could see it in Pike's glassy-eyed gaze and the slump of Jim's shoulders. But still he dropped to his knees, and reached out with two fingers to check his pulse.

"He's gone, Bones." Jim said in a gravelly voice.

Bones sat back, kneeling beside Jim; even when he'd checked Pike over, it had been Jim he was worrying about. He was too tense, and too pale, and his eyes were a worrying shade of grey. Bones set a broad hand on Jim's back, smoothing out the grey Dress Uniform, but he didn't even flinch.

"Jim, I've gotta go," Bones whispered, but he wasn't even sure he was listening. "I'll meet you back-"

"At the apartment," Jim finished for him, although that wasn't what Bones was about to suggest. "Right. Go do your job."

Bones gave a soft sigh, rising to his feet. This wasn't easy for him either; Jim hadn't been the only one close to Pike. But he knew Jim had it hard, and he'd do his best to go easy on him.

"I'll see you soon, Jim." He said, before turning and walking towards a group of bleeding and bruised Starfleet Officers.

He only made it three steps before Jim stopped him.

"I love you, Bones."

He hadn't moved, but at least now Jim was looking at him. Bones didn't make a move to approach him, but he did turn to look at him, giving him a long, solemn look.

"I love you too, Jim." He answered.

Jim gave a nod, and they both went back to their business.

~*~

When Bones got back to the apartment, a good four hours later, the lights were off completely.

"Lights, 50%." Bones said, almost warily, as he stood in the doorway.

The room was trashed.

And by trashed, Bones meant _completely_ trashed.

There was glass on the floor, and something resembling a bourbon stain soaking into the carpet; he'd know that smell anywhere. The kitchenette was trashed, with bits of china scattered all over the floor. The coffee table in the living room had been flipped over, and the TV showed nothing but a blank blue screen.

It took Bones a little while to hear the snuffling coming from behind the arm chair.

"Jim," He sighed, when he stepped around the back to see him sobbing, his hands shaking as blood dripped from his palm. He looked at Bones with wide, wet eyes, like a deer caught in headlights, and then he looked away. That slump to his shoulders was something Bones had only seen a handful of times, but he easily recognised; Jim was ashamed of himself. And he was hurting, hurting way too much for even Bones, one of the best doctors in the 'Fleet, to fix.

"Let me see that." Bones murmured, crouching down till he reached Jim's level. He took hold of

Bones kept a med kit in almost every cupboard, drawer, nook and cranny in their apartment. He was pretty close to just strapping one to Jim's back, but instead he reached for the one under the sofa.

"You drunk?" He asked, as he opened it up and pulled out a few swabs.

Jim sniffled. "Does it matter?"

The slur to his words told him that Jim was indeed drunk. And so he decided to act as if he had answered in the affirmative.

"Good," He said, "'Cause this is gonna hurt."

He wiped down Jim's hand, and heard him hiss at the sting of the swab against his open skin. There were a few shards of glass in there, and Bones used a pair of tweezers to extract them and drop them to a safer location on the floor, out of Jim's general vicinity. He pressed the swabs back against his hand as blood oozed out of the freshly reopened wound, and bandaged him up.

"You broke my last dermal regenerator," Bones told him. "Remember? You crushed it with your bag fat ass."

Jim snickered, but his smile lacked the warmth in his eyes. He gave a thick swallow, and looked down at his hand.

"I miss him." Jim said softly.

Bones missed him too, if only because he'd have known exactly what to say right now to make it better. Bones didn't really have a way with words; gestures, however, he could do.

He set his hand on Jim's shoulder, which conveyed more meaning than any word could.

"Let's get you to bed," Bones said. Jim was easy enough to lift up, even if he was a bit of a dead weight; at least he was pliant. Bones managed to get him to their room, stripping him of his jacket, shoes and trousers before bundling him into bed. The grey dress trousers were speckled with blood, as were Bones', and were now destined for the trash.

Bones plan now was: get Jim to sleep, remove the harzards, and then clean up the apartment so that when Jim woke, he would have as little a reminder of what he'd done the night before as was possible.

Bones wasn't even out the room when Jim stopped him. It was amazing how Jim could say a simple sentence, and ground Bones completely.

"Please stay."

It took Bones no less than thirty seconds to cross the room, strip himself of his dress uniform, turn the lights down and clamber into bed beside Jim.

His captain fit into his arms like a complimentary puzzle piece, Jim's head on his shoulder and their chests pressed together, their legs completely tangled. Bones pretended not to notice whilst Jim siffled into his clavicle, knowing he'd be grateful in the morning.

It was only when Jim's breathing evened out that Bones fell asleep.


	4. IV: Easy fight and easy forgivness

**Summary for the Chapter:**

> It's not even really a fight, and it's over before it ever really began.

The crew of the Enterprise knew not to get too close to McCoy when he was pissed, and right now, he was really, _really_ pissed. He pottered about med bay grumbling to himself about 'damn captain's under his breath, and he barked at anyone who got in his way.

One of he nurses had seen the exchange between them in the shuttle bay, and of course she had told her friends down in med bay. So now everyone knew that Jim was the cause of this grumbling, as he so often was.

When said Captain marched right into med bay, everybody stopped.

Well, except McCoy. It was as if he had radar, because he did not look up.

"Doctor McCoy," Jim greeted him, but McCoy still didn't look up from the biobed he was callibrating.

" _Captain_ ," He replied icily.

Jim deflated a little, and reached out to grab McCoy's upper arm. "Bones,"

It was only because he was so persistant that McCoy looked up. Or at least, that's what he told himself. It definitely wasn't because of how desperate he sounded.

"Jim, I'm busy." He replied curtly, moving around the edge of the bed to the next one when the display lit up and flashed a couple of times. Jim, like a little lost puppy, followed along behind him. The nurses turned back to their work, but they kept their eyes on the couple.

"Bones, please," Jim sighed. "I know I was a jackass, but-"

"Oh so you know, do you?" McCoy snapped, turning to face Jim abruptly. "Well that makes me feel so much better. At least you _know_ that you're being a total ass."

Jim scowled. "What have I done wrong, Bones? Except acting like the Captain, which, funnily enough, I am?"

McCoy gave a hard swallow, and walked along to the next bed. He could've just done a mass callibration at the computer in his office, but he was looking for something to keep his hands busy. And anyway, Jim didn't need to know that.

"Bones," Jim prompted after a short pause.

"You've took the most dangerous, and stupid, might I add, mission the 'Fleet could ever dream up, and all because your new daddy died." The way Jim's face crumpled told him he'd taken a step too far. He kept going anyways. "You're going to take this whole crew- 400 people, Jim! - into Klingon space, just to avenge his death. And don't try to tell me you're doing this for Earth because I know you, Jim. You're going to go down there, and you're going to get yourself killed. And then where'll I be?"

McCoy didn't look at him, but Jim stared, blue eyes boring into his skull. After a short puse, Bones added in a husky voice, "And I haven't seen you since you trashed the apartment. You were up and away before I was, Jim. This is the longest conversation I've had with you in two days."

"I'm sorry." Jim murmured, but McCoy shook his head.

"Doesn't matter, Jim. Do what you please. You always do, anyway."

"Bones, I-" McCoy moved to the next bed, away from Jim as he spoke.

"Will that be all, Captain?"

It wasn't as icy as before, but rather, Bones sounded more defeated than anything. The pair regarded each other for a long time. Jim looked at the floor, and then he looked back up at the good doctor, and in one swif movement, he pressed their lips together.

"I'm sorry, Bones." He murmured, when he pulled away.

McCoy's eyes were on the floor. "I'm sorry too, Jim."

It was as close to an "I love you" as either of them were going to get right now, but it'd do. When Jim murmured that he had to go to the bridge, McCoy nodded.

"Go do your job, Jim." McCoy told him.

And even though they could both hold a grudge till they were blue in the face, they were each forgiven just like that.

**Author's Note:**

> Apologies for typos and errors and the such like.


End file.
